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-rw-r--r--libcrystfel/src/beam-parameters.h8
-rw-r--r--libcrystfel/src/dirax.c12
-rw-r--r--libcrystfel/src/dirax.h2
-rw-r--r--libcrystfel/src/image.h3
-rw-r--r--libcrystfel/src/index.c127
-rw-r--r--libcrystfel/src/index.h12
-rw-r--r--libcrystfel/src/mosflm.c15
-rw-r--r--libcrystfel/src/mosflm.h2
-rw-r--r--libcrystfel/src/reax.c10
-rw-r--r--libcrystfel/src/reax.h13
-rw-r--r--libcrystfel/src/stream.c1
11 files changed, 168 insertions, 37 deletions
diff --git a/libcrystfel/src/beam-parameters.h b/libcrystfel/src/beam-parameters.h
index 8212811b..de777deb 100644
--- a/libcrystfel/src/beam-parameters.h
+++ b/libcrystfel/src/beam-parameters.h
@@ -3,11 +3,11 @@
*
* Beam parameters
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2013-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2010,2012 Thomas White <taw@physics.org>
+ * 2010,2012-2013 Thomas White <taw@physics.org>
* 2012 Chunhong Yoon
*
* This file is part of CrystFEL.
@@ -34,6 +34,8 @@
#include <config.h>
#endif
+struct beam_params;
+
#include "hdf5-file.h"
struct beam_params
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index fc185fd4..e6ff36b1 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -626,27 +626,31 @@ int run_dirax(struct image *image, IndexingPrivate *ipriv)
}
-IndexingPrivate *dirax_prepare(IndexingMethod indm, UnitCell *cell,
+IndexingPrivate *dirax_prepare(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
struct beam_params *beam, float *ltl)
{
struct dirax_private *dp;
int need_cell = 0;
- if ( indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
- if ( indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
+ if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
+ if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
if ( need_cell && (cell == NULL) ) {
ERROR("DirAx needs a unit cell for this set of flags.\n");
return NULL;
}
+ /* Flags that DirAx knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
+ | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS;
+
dp = malloc(sizeof(struct dirax_private));
if ( dp == NULL ) return NULL;
dp->ltl = ltl;
dp->template = cell;
- dp->indm = indm;
+ dp->indm = *indm;
return (IndexingPrivate *)dp;
}
diff --git a/libcrystfel/src/dirax.h b/libcrystfel/src/dirax.h
index 9e746a1b..6be8451a 100644
--- a/libcrystfel/src/dirax.h
+++ b/libcrystfel/src/dirax.h
@@ -37,7 +37,7 @@
extern int run_dirax(struct image *image, IndexingPrivate *ipriv);
-extern IndexingPrivate *dirax_prepare(IndexingMethod indm,
+extern IndexingPrivate *dirax_prepare(IndexingMethod *indm,
UnitCell *cell, const char *filename,
struct detector *det,
struct beam_params *beam, float *ltl);
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 91950e76..3739c01f 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -42,6 +42,7 @@
#include "detector.h"
#include "reflist.h"
#include "crystal.h"
+#include "index.h"
/* Structure describing a feature in an image */
@@ -79,6 +80,7 @@ typedef struct _imagefeaturelist ImageFeatureList;
*
* Crystal **crystals;
* int n_crystals;
+ * IndexingMethod indexed_by;
*
* struct detector *det;
* struct beam_params *beam;
@@ -128,6 +130,7 @@ struct image {
Crystal **crystals;
int n_crystals;
+ IndexingMethod indexed_by;
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 28f33388..f65265ae 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -65,20 +65,26 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
for ( n=0; n<nm; n++ ) {
+ int i;
+ IndexingMethod in;
+
+ in = indm[n];
+
switch ( indm[n] & INDEXING_METHOD_MASK ) {
case INDEXING_DIRAX :
- iprivs[n] = dirax_prepare(indm[n], cell, filename, det,
+ iprivs[n] = dirax_prepare(&indm[n], cell, filename, det,
beam, ltl);
break;
case INDEXING_MOSFLM :
- iprivs[n] = mosflm_prepare(indm[n], cell, filename, det,
+ iprivs[n] = mosflm_prepare(&indm[n], cell, filename, det,
beam, ltl);
break;
case INDEXING_REAX :
- iprivs[n] = reax_prepare(cell, filename, det, beam);
+ iprivs[n] = reax_prepare(&indm[n], cell, filename, det,
+ beam, ltl);
break;
default :
@@ -90,6 +96,25 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
if ( iprivs[n] == NULL ) return NULL;
+ STATUS("Prepared indexing method %i: %s\n",
+ n, indexer_str(indm[n]));
+
+ if ( in != indm[n] ) {
+ ERROR("Note: flags were altered to take into account "
+ "the limitations of the indexing method.\n");
+ }
+
+ for ( i=0; i<n; i++ ) {
+ if ( indm[i] == indm[n] ) {
+ ERROR("Duplicate indexing method.\n");
+ ERROR("Have you specified some flags which "
+ "aren't accepted by one of your "
+ "chosen indexing methods?\n");
+ return NULL;
+ }
+ }
+
+
}
iprivs[n] = NULL;
@@ -160,7 +185,7 @@ void map_all_peaks(struct image *image)
/* Return non-zero for "success" */
static int try_indexer(struct image *image, IndexingMethod indm,
- IndexingPrivate *ipriv)
+ IndexingPrivate *ipriv)
{
switch ( indm & INDEXING_METHOD_MASK ) {
@@ -206,14 +231,8 @@ void index_pattern(struct image *image,
n++;
}
-}
-
-/* Set the default indexer flags. May need tweaking depending on the method */
-static IndexingMethod defaults(IndexingMethod a)
-{
- return a | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_PEAKS
- | INDEXING_USE_LATTICE_TYPE;
+ image->indexed_by = indms[n];
}
@@ -242,6 +261,14 @@ static IndexingMethod set_axes(IndexingMethod a)
}
+/* Set the indexer flags for "combination mode" ("--cell-reduction=reduce") */
+static IndexingMethod set_comb(IndexingMethod a)
+{
+ return (a & ~INDEXING_CHECK_CELL_AXES)
+ | INDEXING_CHECK_CELL_COMBINATIONS;
+}
+
+
/* Set the indexer flags for "use no lattice type information" */
static IndexingMethod set_nolattice(IndexingMethod a)
{
@@ -249,6 +276,71 @@ static IndexingMethod set_nolattice(IndexingMethod a)
}
+/* Set the indexer flags for "use lattice type information" */
+static IndexingMethod set_lattice(IndexingMethod a)
+{
+ return a | INDEXING_USE_LATTICE_TYPE;
+}
+
+
+char *indexer_str(IndexingMethod indm)
+{
+ char *str;
+
+ str = malloc(32);
+ if ( str == NULL ) {
+ ERROR("Failed to allocate string.\n");
+ return NULL;
+ }
+ str[0] = '\0';
+
+ switch ( indm & INDEXING_METHOD_MASK ) {
+
+ case INDEXING_NONE :
+ strcpy(str, "none");
+ return str;
+
+ case INDEXING_DIRAX :
+ strcpy(str, "dirax");
+ break;
+
+ case INDEXING_MOSFLM :
+ strcpy(str, "mosflm");
+ break;
+
+ case INDEXING_REAX :
+ strcpy(str, "reax");
+ break;
+
+ default :
+ ERROR("Unrecognised indexing method %i\n", indm);
+ strcpy(str, "(unknown)");
+ break;
+
+ }
+
+ if ( indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
+ strcat(str, "-comb");
+ } else if ( indm & INDEXING_CHECK_CELL_AXES ) {
+ strcat(str, "-axes");
+ } else {
+ strcat(str, "-raw");
+ }
+
+ if ( !(indm & INDEXING_CHECK_PEAKS) ) {
+ strcat(str, "-bad");
+ }
+
+ if ( indm & INDEXING_USE_LATTICE_TYPE ) {
+ strcat(str, "-latt");
+ } else {
+ strcat(str, "-nolatt");
+ }
+
+ return str;
+}
+
+
IndexingMethod *build_indexer_list(const char *str)
{
int n, i;
@@ -263,14 +355,13 @@ IndexingMethod *build_indexer_list(const char *str)
for ( i=0; i<n; i++ ) {
if ( strcmp(methods[i], "dirax") == 0) {
- list[++nmeth] = defaults(INDEXING_DIRAX);
+ list[++nmeth] = INDEXING_DEFAULTS_DIRAX;
} else if ( strcmp(methods[i], "mosflm") == 0) {
- list[++nmeth] = defaults(INDEXING_MOSFLM);
+ list[++nmeth] = INDEXING_DEFAULTS_MOSFLM;
} else if ( strcmp(methods[i], "reax") == 0) {
- /* ReAx doesn't need any cell check */
- list[++nmeth] = set_raw(defaults(INDEXING_REAX));
+ list[++nmeth] = INDEXING_DEFAULTS_REAX;
} else if ( strcmp(methods[i], "none") == 0) {
list[++nmeth] = INDEXING_NONE;
@@ -282,9 +373,15 @@ IndexingMethod *build_indexer_list(const char *str)
} else if ( strcmp(methods[i], "bad") == 0) {
list[nmeth] = set_bad(list[nmeth]);
+ } else if ( strcmp(methods[i], "comb") == 0) {
+ list[nmeth] = set_comb(list[nmeth]); /* Default */
+
} else if ( strcmp(methods[i], "axes") == 0) {
list[nmeth] = set_axes(list[nmeth]);
+ } else if ( strcmp(methods[i], "latt") == 0) {
+ list[nmeth] = set_lattice(list[nmeth]);
+
} else if ( strcmp(methods[i], "nolatt") == 0) {
list[nmeth] = set_nolattice(list[nmeth]);
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index a54691b4..7d6656d5 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -38,11 +38,22 @@
#endif
+#include "beam-parameters.h"
#include "cell.h"
#include "image.h"
#include "detector.h"
+#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
+ | INDEXING_CHECK_CELL_COMBINATIONS)
+
+#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \
+ | INDEXING_CHECK_CELL_COMBINATIONS \
+ | INDEXING_USE_LATTICE_TYPE)
+
+#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_CHECK_PEAKS)
+
/**
* IndexingMethod:
* @INDEXING_NONE: No indexing to be performed
@@ -84,6 +95,7 @@ typedef enum {
typedef void *IndexingPrivate;
extern IndexingMethod *build_indexer_list(const char *str);
+extern char *indexer_str(IndexingMethod indm);
extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename,
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 98d4280d..22606fa4 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -798,28 +798,33 @@ int run_mosflm(struct image *image, IndexingPrivate *ipriv)
}
-IndexingPrivate *mosflm_prepare(IndexingMethod indm, UnitCell *cell,
+IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
struct beam_params *beam, float *ltl)
{
struct mosflm_private *mp;
int need_cell = 0;
- if ( indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
- if ( indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
- if ( indm & INDEXING_USE_LATTICE_TYPE ) need_cell = 1;
+ if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
+ if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
+ if ( *indm & INDEXING_USE_LATTICE_TYPE ) need_cell = 1;
if ( need_cell && (cell == NULL) ) {
ERROR("MOSFLM needs a unit cell for this set of flags.\n");
return NULL;
}
+ /* Flags that MOSFLM knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
+ | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
+ | INDEXING_USE_LATTICE_TYPE;
+
mp = malloc(sizeof(struct mosflm_private));
if ( mp == NULL ) return NULL;
mp->ltl = ltl;
mp->template = cell;
- mp->indm = indm;
+ mp->indm = *indm;
return (IndexingPrivate *)mp;
}
diff --git a/libcrystfel/src/mosflm.h b/libcrystfel/src/mosflm.h
index 4bb26afc..a87232b6 100644
--- a/libcrystfel/src/mosflm.h
+++ b/libcrystfel/src/mosflm.h
@@ -40,7 +40,7 @@
extern int run_mosflm(struct image *image, IndexingPrivate *ipriv);
-extern IndexingPrivate *mosflm_prepare(IndexingMethod indm, UnitCell *cell,
+extern IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
const char *filename,
struct detector *det,
struct beam_params *beam, float *ltl);
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index f454503c..3460a4f2 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -1084,7 +1084,7 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
}
-IndexingPrivate *reax_prepare(IndexingMethod indm, UnitCell *cell,
+IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
struct beam_params *beam, float *ltl)
{
@@ -1100,6 +1100,12 @@ IndexingPrivate *reax_prepare(IndexingMethod indm, UnitCell *cell,
p = calloc(1, sizeof(*p));
if ( p == NULL ) return NULL;
+ /* Flags that ReAx knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS;
+
+ /* Flags that ReAx requires */
+ *indm |= INDEXING_USE_LATTICE_TYPE;
+
p->angular_inc = deg2rad(1.0);
/* Reserve memory, over-estimating the number of directions */
@@ -1160,7 +1166,7 @@ IndexingPrivate *reax_prepare(IndexingMethod indm, UnitCell *cell,
p->r_plan = fftw_plan_dft_2d(p->cw, p->ch, p->r_fft_in, p->r_fft_out,
1, FFTW_MEASURE);
- p->indm = indm;
+ p->indm = *indm;
return (IndexingPrivate *)p;
}
diff --git a/libcrystfel/src/reax.h b/libcrystfel/src/reax.h
index af383e29..657a2cdf 100644
--- a/libcrystfel/src/reax.h
+++ b/libcrystfel/src/reax.h
@@ -33,15 +33,16 @@
#include <config.h>
#endif
+#include "index.h"
#include "cell.h"
#include "beam-parameters.h"
#include "detector.h"
#ifdef HAVE_FFTW
-extern IndexingPrivate *reax_prepare(UnitCell *cell, const char *filename,
- struct detector *det,
- struct beam_params *beam);
+extern IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
+ const char *filename, struct detector *det,
+ struct beam_params *beam, float *ltl);
extern void reax_cleanup(IndexingPrivate *pp);
@@ -49,9 +50,9 @@ extern int reax_index(struct image *image, IndexingPrivate *p);
#else /* HAVE_FFTW */
-static IndexingPrivate *reax_prepare(UnitCell *cell, const char *filename,
- struct detector *det,
- struct beam_params *beam)
+static IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
+ const char *filename, struct detector *det,
+ struct beam_params *beam, float *ltl)
{
return NULL;
}
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 842c90b9..692a860a 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -199,6 +199,7 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
fprintf(st->fh, CHUNK_START_MARKER"\n");
fprintf(st->fh, "Image filename: %s\n", i->filename);
+ fprintf(st->fh, "indexed_by = %s\n", indexer_str(i->indexed_by));
if ( i->det != NULL ) {
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 10:08:10 +0000